Coding style¶

`bin/` scripts: environment variables or command line arguments?¶

When writing scripts (Python, R, Bash) for the workflow, you have the choice between loading environment variables from inside the script, or parsing command line arguments.

As a rule of thumb, use environment variables when you don’t expect the script to be reused outside the workflow, and command line arguments with strong input validation when you want to make the script more portable.

Cylc¶

In general, follow Cylc Style Guidelines . When creating tasks, set the [meta] title and description fields to describe what the task does. You can also add custom field like categories if you want.

Use uppercase for:

family tasks (notably the conda ones, e.g. CONDA_OPENMS),
global environment variables set in [runtime][root] and broadcasted ones (e.g. RAWFILE_STEM).

Use lowercase for:

local environment variables set in [environment] blocks inside tasks.
task names.

Add None before the name of inherited family tasks to make the task in question appear at the root when using the TUI or GUI. Otherwise, the task will be nested under the family task. The exception are InfluxDB tasks, which are always nested under the INFLUXDB family task.

When using global environment variables or Jinja2 template variables to build CLI arguments, do it in the [environment] block of the task, not in the script itself:

flow.cylc¶

    [[trim_spectra]]
        inherit = None, CONDA_OPENMS
        script = """
            trimms ${mzml} ${n_start} ${n_end}
        """
        [[[environment]]]
            mzml = ${MAIN_RESULTS_DIR}/${RAWFILE_STEM}.mzML
            n_start = {{ cfg__trim_values[0] }}
            n_end = {{ cfg__trim_values[1] }}
        [[[meta]]]
            title = Trim Spectra
            description = """
                Remove the first `n_start` and last `n_end` scans from the mzML file. This is useful
                if the shape of the flowgram is not stable at the beginning or end of the run.
            """
            categories = bioinformatics

Python¶

Python code should follow the PEP 8 style guide. The Black code formatter should be used to automatically format the code.

You should also use a linter / static code analyser like Pylint to catch potential bugs, commented out code, code smells, etc.

Bash¶

[TODO]

R¶